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Table 1 Genome-wide Significant SNPs from Novel HLA Locus Identified in Imputation GWAS

From: Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia

SNP Position Minor allele Nearest gene P imputeda Rep case MAF b Rep Cont. MAF c P replicationd P metae OR (95 % CI) combinedf P adjustedg
rs614549 31948604 C SLC44A4 5.74 × 10−05 0.32 0.38 5.87 ×10−05 2.09 × 10−08 0.80 (0.73, 0.87) 0.26
rs7887 31972526 A EHMT2 1.18 × 10−05 0.31 0.37 5.84 ×10−05 3.70 × 10−09 0.78 (0.71, 0.86) NA
rs2844452 31990003 C C2 1.69 × 10−05 0.42 0.47 0.00071 4.55 × 10−08 0.81 (0.74, 0.88) 0.26
rs3020644 32002605 G C2 1.13 × 10−05 0.36 0.41 0.00062 2.68 × 10−08 0.80 (0.73, 0.87) 0.28
rs2280774 32036670 T NELFE 1.11 × 10−05 0.29 0.34 0.00096 3.89 × 10−08 0.81 (0.74, 0.89) 0.83
rs3117116 32474995 C BTNL2 9.15 × 10−08 0.15 0.13 0.038 2.65 × 10−08 1.25 (1.10, 1.41) 0.02
  1. a P-value from imputation analysis under additive model using discovery GWAS samples
  2. bMinor allele frequency among replication cases (878)
  3. cMinor allele frequency among replication controls (2017)
  4. d P-value from additive model among replication cases and controls
  5. e P-value from meta-analysis of discovery imputation and replication
  6. fOdds ratio (OR) and 95 % CI for joint analysis comparing subset of GWAS cases (1498) and replication cases (878) to replication controls (2017) based on observed genotypes; GWAS cases were genotyped at same time as replication cases and controls
  7. g P-value from joint analysis as in (f) with adjustment for rs7887